It is a bit odd that a scout qualified on 100t type S scout/couriers and x-boats can pilot a dreadnaught while a 95t shuttle 'pilot' can not.
Especially since piloting any of them is probably no more difficult than playing a real world console/PC space sim...
I assume the key underlying skill for Pilot and Ships Boats, isn't stick flying the vessel, but running the jump and maneuver drives.
IMTU, the jumping isn't plot the course, push a button, and relax for a week. I assume it is a complex engineering task (to explain why pilots earn a 50% premium over engineers; their job is more technically demanding) requiring
1) measuring and interpreting data taken from the ongoing jump reaction,
2) simulating the system,
3) making adjustments to the drive operation,
4) repeat over the term of the jump
in order to arrive as intended. I figure quantum effects and parasitics require the reaction be monitored and managed.
Ships Boat skill is also a trained engineer, but their background doesn't go beyond monitoring and managing reactions in small maneuver drives. I'd let Ships Boat skill control a 100dT ship on an intrasystem journey at -1 skill, but never get the vessel into jump.
My model for these guys aren't modern aircraft pilots, rather I assume they have technical smarts like NASA astronauts, with the pilots being the best of the best.
I think you are right though about the Scout to Dreadnought leap though, just in practice it doesn't come up. Maybe Pilot skill should be a cascade skill with different skills for each factor of 10 in tonnage.